Random files missing from every clone of a repository

Every time I clone a respository hosted on GitHub to my local IDE environment, there are random files missing (nothing exotic; these are very basic files like .html and .css and image files). Inspection of the actual directory on my computer shows these files missing. 

If I trash the directory and re-clone the same respository, a different selection of random files will be missing each time. It’s never the same combination twice. 

This issue has been plaguing me for a couple weeks now, and affects any and every repository I fork and clone.

Eventually, I give up trying to get a complete clone, and download a zip of the repository and manually backfill the missing files into the local directory so I can proceed with my lesson.

I’m fairly new to this and I realize that there are many variables involved, however I thought I would start here in case this is an issue that others have encountered (and easily resolved). Thank you!

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What tool are you using to clone the repository? Can you give us the exact steps you follow to reproduce the problem?